Ryo Yokoyama

Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein | PNAS www.pnas.org/doi/10.1073/... @pnas.org

Once again, it’s a great honor to receive the TPJ-PSNA Early Career Award! My heartfelt thanks to all the mentors, colleagues, and collaborators who have supported me along the way.

Cyanophycinase is required for heterotrophy in cyanobacteria Cyanophycin is a biopolymer of arginine and aspartate, and it is found in various prokaryotes. Two key enzymes of cyanophycin metabolism are cyanophycin synthase (CphA) producing cyanophycin, and cyan...

Cyanophycinase is required for heterotrophy in cyanobacteria - Journal of Biological Chemistry www.jbc.org/article/S002...

Editing of rice PSEUDO-ETIOLATION IN LIGHT microProtein genes promotes chloroplast development academic.oup.com/plcell/artic...

A perspective: A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species (Planta 149, 78–90) - Planta The model of C3 photosynthesis of Farquhar et al. (1980) integrated knowledge of the functioning of the biochemical components of photosynthetic carbon assimilation in C3 plants. The model linked equations describing activated Rubisco kinetics with those on the stoichiometry of the photosynthetic carbon reduction cycle and the photorespiratory carbon oxidation cycle, particularly on their energetic (electron transport, ATP synthesis and NADPH) requirements. It included temperature dependencies of these processes and combined them with a semi-empirical equation for the dependence of potential electron transport rate on absorbed irradiance. The model aimed to match generalized observations of photosynthetic gas exchange of leaves with predictions from this mathematical summary of photosynthesis. In this model, we introduced the hypothesis that the rate of Rubisco carboxylation could not exceed the capacity for RuP2 regeneration or the enzymatic capacity to consume RuP2, and that the system behaved as a teeter-totter (see-saw) with a sharp transition from one limiting state to the other. We suggested that to model genotypic and phenotypic variations amongst leaves most parameters could be assigned a priori and only the maximum Rubisco activity (Vcmax) and the maximal electron transport rate, Jmax, needed to be varied. This simplicity of use led to the wider spread application and success of the model.

A perspective: A biochemical model of photosynthetic CO2 assimilation in leaves of C3 species link.springer.com/article/10.1...

Large-scale mining of plant genomes unlocks the diversity of oxidosqualene cyclases - Nature Chemical Biology In plants, oxidosqualene cyclases (OSCs) perform a highly complex single reaction to generate the basis of all triterpenoid diversity. Here the authors leverage genome mining and transient expression to uncover multiple evolutionary and mechanistic insights for OSCs across the plant kingdom.

Large-scale mining of plant genomes unlocks the diversity of oxidosqualene cyclases www.nature.com/articles/s41... @natchembio.nature.com

CYP81D11, an apocarotenoid-responsive cytochrome P450, enhances photosynthesis and stress tolerance in plants High expression of the cytochrome P450 CYP81D11 leads to high tolerance to abiotic stresses by increasing photosynthetic capacity and preventing accumulati

CYP81D11, an apocarotenoid-responsive cytochrome P450, enhances photosynthesis and stress tolerance in plants academic.oup.com/plphys/artic... @plantphys.bsky.social

Photorespiration and plant immunity: Interactions and implications under a changing climate Climate change has profound impacts on plant growth, productivity, and immunity. Photosynthesis, a key biological process that sequesters atmospheric …

Photorespiration and plant immunity: Interactions and implications under a changing climate www.sciencedirect.com/science/arti...

Redox-regulated plastoglobule ABC1K1–ABC1K3 kinase complex controls plastoquinone mobilization for chloroplast photosynthetic adaptation to red light Summary: In Arabidopsis, a redox-regulated plastoglobule ABC1K1–ABC1K3 kinase complex responds to red light-induced plastoquinone (PQ) pool reduction. Activated thylakoid oxidoreductase LTO1 oxidizes ...

Redox-regulated plastoglobule ABC1K1–ABC1K3 kinase complex controls plastoquinone mobilization for chloroplast photosynthetic adaptation to red light www.cell.com/molecular-pl... @mplantpcom.bsky.social

Light-mediated balances and trade-offs in plant energy and resource management Abstract. Light is a central environmental signal that coordinates plant development, metabolism, and stress responses. By integrating external cues with i

Light-mediated balances and trade-offs in plant energy and resource management academic.oup.com/jxb/article/... @jxbotany.bsky.social

Discovery of iridoid cyclase completes the iridoid pathway in asterids - Nature Plants Iridoids are terpenoid metabolites found in thousands of plants. Using single-cell transcriptomics, the authors discovered an unexpected enzyme that has been neofunctionalized to catalyse the cyclization required to form the iridoid scaffold.

Discovery of iridoid cyclase completes the iridoid pathway in asterids www.nature.com/articles/s41... @natplants.nature.com

Move over endosymbionts, peroxisomes pass electrons too portlandpress.com/biochemsoctr...

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae Cellular homeostasis is maintained by the balance between energy production and breakdown and is fundamental to all forms of life. The conserved, ancient target of rapamycin (TOR) kinase is a central ...

TOR inhibition drives accumulation of amino acids through transcriptional activation in algae www.biorxiv.org/content/10.1...

Rubisco-Centric Strategies for Carbon Conservation in Synthetic Biology The escalating global climate crisis urgently demands biomanufacturing technologies with higher carbon efficiency. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), the central enzyme catalyzing carbon dioxide fixation in the Calvin–Benson cycle, exhibits low efficiency, thereby limiting its industrial application. This review summarizes fundamental Rubisco research, laying the foundation for its efficiency-enhancing engineering and biomanufacturing applications. We first outline the discovery, systematic classification, and molecular evolution of Rubisco, and then elucidate the structural dynamics underlying its activation and inhibition mechanisms. Subsequently, we provide the first systematic synthesis of five enzyme-efficiency enhancement strategies, spanning classical directed evolution to artificial intelligence-driven rational design. Recent advances in the utilization of Rubisco by autotrophic and heterotrophic microorganisms for the synthesis of biobased products are also critically examined. The resulting cross-scale design framework integrates evolutionary biology, structural dynamics, and synthetic biology, offering an extensible paradigm for sustainable, carbon-neutral biomanufacturing.

Rubisco-Centric Strategies for Carbon Conservation in Synthetic Biology | Journal of Agricultural and Food Chemistry pubs.acs.org/doi/10.1021/...

High conservation of translation-enabling RNA editing sites in hyper-editing ferns implies they are not selectively neutral academic.oup.com/mbe/article/... @molbioevol.bsky.social

FEBS Press Phylogenetic analyses of glutamine synthetase (GS) in seed plants revealed that all three major evolutionary lineages (GS2, GS1a, and GS1b) must have been present in the common ancestor, with GS2 bei....

Phylogenetic reconciliation provides new insights into the evolutionary diversification of the glutamine synthetase gene family in seed plants febs.onlinelibrary.wiley.com/doi/10.1111/... @febsj.bsky.social

Previously unrecognized diversity of far-red light-using terrestrial green algae and cyanobacteria Oxygenic photosynthesis in cyanobacteria, algae, and plants typically relies on visible light, but some lineages can utilize far-red light (FRL, wavel…

Previously unrecognized diversity of far-red light-using terrestrial green algae and cyanobacteria www.sciencedirect.com/science/arti... @cp-iscience.bsky.social

Drastic Reduction in Cytochrome b6/f Complex Confers Robust PSI Photoprotection Under Fluctuating Light at the Expense of Photosynthetic Capacity Plants in natural habitats frequently encounter fluctuating light (FL), which can lead to photoinhibition of Photosystem I (PSI), thereby limiting photosynthetic productivity. The cytochrome (Cyt) b6...

Drastic Reduction in Cytochrome b6/f Complex Confers Robust PSI Photoprotection Under Fluctuating Light at the Expense of Photosynthetic Capacity onlinelibrary.wiley.com/doi/10.1111/...

Further evidence supporting the existence and accumulation of triacylglycerol and acylplastoquinol in cyanobacteria academic.oup.com/plphys/artic... @plantphys.bsky.social

Eukaryogenesis From FECA to LECA: Radical Steps Along the Way How did the last eukaryotic common ancestor (LECA) population evolve? Recent evidence shows an Asgard archaeon-like organism acquiring a bacterium, the future mitochondrion, going from symbiosis to e...

Eukaryogenesis From FECA to LECA: Radical Steps Along the Way onlinelibrary.wiley.com/doi/10.1002/...

Disturbed RNA editing in MORF3-deficient Arabidopsis mitochondria leads to impaired assembly of complex I RNA editing at specific mitochondrial transcript sites in Arabidopsis thaliana is crucial for Complex I assembly and stability, with deficiencies leading t

Disturbed RNA editing in MORF3-deficient Arabidopsis mitochondria leads to impaired assembly of complex I academic.oup.com/plphys/artic... @plantphys.bsky.social

The isoprenoid biosynthesis enzyme HDS participates in chloroplast RNA editing Abstract. Post-transcriptional RNA editing and retrograde signaling in chloroplasts are crucial for coordinating gene expression between chloroplasts and t

The isoprenoid biosynthesis enzyme HDS participates in chloroplast RNA editing academic.oup.com/jxb/article-... @jxbotany.bsky.social

Carbon Dioxide Release During Photosynthesis: Connecting Gas Exchange Behavior With Biochemistry This review clarifies the metabolic origin of light-driven CO₂ release, highlighting the dominant role of the cytosolic G6P shunt via the oxidative pentose phosphate pathway, resolving long-standing ...

Carbon Dioxide Release During Photosynthesis: Connecting Gas Exchange Behavior With Biochemistry onlinelibrary.wiley.com/doi/10.1111/...

Time-resolved targeted metabolomics shows an abrupt switch from Calvin-Benson-Bassham cycle to tricarboxylic acid cycle when the light is turned off - Photosynthesis Research In leaves, major CO₂ fluxes alternate between fixation by the Calvin-Benson-Bassham (CBB) cycle during light and release by the tricarboxylic acid (TCA) cycle in darkness. The speed at which leaf metabolism transitions between these pathways likely influences plant tolerance to fluctuating light conditions. To investigate these rapid metabolic shifts, we exposed leaves to ¹³CO₂ for 20 min to establish a quasi-steady state before abruptly turning off the light while maintaining ¹³CO₂ feeding. Within 10 s of dark transition, 3-phosphoglycerate levels rose significantly while most other CBB cycle intermediates decreased by more than 90%. Simultaneously, carbon accumulated in alanine, likely via pyruvate. Over the subsequent 10 min, six- and five-carbon TCA cycle intermediates steadily increased. In contrast, four-carbon TCA intermediates peaked at one minute, declined at three minutes, and rose again at 10 min, a pattern mirrored by most measured amino acids. These results reveal an exceptionally rapid metabolic reconfiguration from CO₂ fixation by the CBB cycle in light to TCA cycle activation for energy production in darkness, accompanied by substantial changes in amino acid metabolism.

Time-resolved targeted metabolomics shows an abrupt switch from Calvin-Benson-Bassham cycle to tricarboxylic acid cycle when the light is turned off link.springer.com/article/10.1...

PROTON GRADIENT REGULATION 5 enables efficient C4 photosynthesis under fluctuating light The Proton Gradient Regulation 5 protein supports photosynthetic control and energy-dependent non-photochemical quenching to protect Photosystem I in C4

PROTON GRADIENT REGULATION 5 enables efficient C4 photosynthesis under fluctuating light academic.oup.com/plphys/artic... @plantphys.bsky.social

Allelic variants of IRKI contribute to photosynthetic efficiency by regulating rubisco activase in Populus The discovery of a gene–haplotype module that enhances photosynthesis in poplar reveals molecular targets for improving biomass in perennial woody plants.

Allelic variants of IRKI contribute to photosynthetic efficiency by regulating rubisco activase in Populus academic.oup.com/plphys/artic... @plantphys.bsky.social

Catalytic Droplets: Enzyme Containing Microcompartments Bacterial microcompartments (BMCs) and biomolecular condensates are two different forms of protein compartmentalization with different aims and functional advantages, representing specific designs of sequestering enzymes or segments of metabolic pathways. BMCs...

Catalytic Droplets: Enzyme Containing Microcompartments
link.springer.com/chapter/10.1...

CsAPRR2 regulates cucumber immature fruit color by coordinating chloroplast biogenesis and photosynthesis‐related gene expression This study uncovers a fruit-specific regulatory mechanism of chloroplast biogenesis in cucumber in which the transcription factor CsAPRR2 plays an important role. Through integration of GWAS, transcr...

CsAPRR2 regulates cucumber immature fruit color by coordinating chloroplast biogenesis and photosynthesis‐related gene expression onlinelibrary.wiley.com/doi/10.1111/... @theplantjournal.bsky.social

Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET The turbine dynamics of mitochondrial ATP synthases is an unresolved topic which in situ cryo-ET is poised to answer. Using publicly available tomogram data of vitrified Chlamydomonas reinhardtii cell...

Structural dynamics of mitochondrial ATP synthase in Chlamydomonas reinhardtii revealed by in situ CryoET www.biorxiv.org/content/10.1...

FEBS Press Advances in cryo-EM have revealed the detailed structure of Photosystem II, a key protein complex driving photosynthesis. This review traces the journey from early low-resolution images to high-resol...

Revealing the structure of land plant photosystem II: the journey from negative‐stain EM to cryo‐EM febs.onlinelibrary.wiley.com/doi/10.1002/... @febsletters.bsky.social